Receptor
PDB id Resolution Class Description Source Keywords
3WBD 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ANTI-POLYSIALIC ACID ANTIBODY SINGLE CH FRAGMENT (MAB735) COMPLEXED WITH OCTASIALIC ACID MUS MUSCULUS BETA-SANDWICH IMMUNOGLOBULIN FOLD SINGLE CHAIN FV FRAGMENTPOLYSIALIC ACID ALPHA2-8 LINKED POLYSIALIC ACID IMMUNE SY
Ref.: CRYSTAL STRUCTURE OF ANTI-POLYSIALIC ACID ANTIBODY CHAIN FV FRAGMENT COMPLEXED WITH OCTASIALIC ACID: I INTO THE BINDING PREFERENCE FOR POLYSIALIC ACID. J.BIOL.CHEM. V. 288 33784 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SIA SIA SIA SIA SIA SIA SIA B:301;
Valid;
none;
submit data
2049.75 n/a O=C([...
FLC A:2001;
Invalid;
none;
submit data
189.1 C6 H5 O7 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WBD 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ANTI-POLYSIALIC ACID ANTIBODY SINGLE CH FRAGMENT (MAB735) COMPLEXED WITH OCTASIALIC ACID MUS MUSCULUS BETA-SANDWICH IMMUNOGLOBULIN FOLD SINGLE CHAIN FV FRAGMENTPOLYSIALIC ACID ALPHA2-8 LINKED POLYSIALIC ACID IMMUNE SY
Ref.: CRYSTAL STRUCTURE OF ANTI-POLYSIALIC ACID ANTIBODY CHAIN FV FRAGMENT COMPLEXED WITH OCTASIALIC ACID: I INTO THE BINDING PREFERENCE FOR POLYSIALIC ACID. J.BIOL.CHEM. V. 288 33784 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3WBD - SIA SIA SIA SIA SIA SIA SIA n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 65 families.
1 1X9Q Kd = 0.27 pM FLU C20 H12 O5 c1ccc(c(c1....
2 1SVZ - PRO GLN PHE SER LEU TRP LYS ARG n/a n/a
3 3WBD - SIA SIA SIA SIA SIA SIA SIA n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 1X9Q Kd = 0.27 pM FLU C20 H12 O5 c1ccc(c(c1....
2 1SVZ - PRO GLN PHE SER LEU TRP LYS ARG n/a n/a
3 1H8S Kd = 1.54 uM AIC C16 H19 N3 O4 S CC1([C@@H]....
4 3WBD - SIA SIA SIA SIA SIA SIA SIA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA SIA SIA SIA SIA SIA SIA; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA SIA SIA SLB 1 1
2 SIA SIA SIA SIA SIA SIA SIA 1 1
3 SLB SIA SIA SIA SIA 1 1
4 SLB SIA SIA 1 1
5 SIA SIA 0.985915 1
6 SLB SIA 0.985915 1
7 SIA SIA SIA 0.729412 1
8 SIA SIA GAL 0.659574 0.981132
9 SIA CMO 0.631579 0.87037
10 BGC SIA SIA GAL 0.563636 0.981132
11 SIA SIA GLA BGC 0.563636 0.981132
12 SLB 0.558442 0.826923
13 SIA 0.558442 0.826923
14 MNA 0.5375 0.851852
15 SIA SIA GAL NGA GAL SIA 0.529915 0.981132
16 SIA SIA GAL NGA GAL 0.525424 0.981132
17 GAL SIA 0.516129 0.907407
18 SIA GAL 0.510638 0.924528
19 SIA GAL SIA GLC NGA 0.504065 0.981132
20 SIA GAL SIA BGC NGA 0.504065 0.981132
21 SIA 2FG 0.494845 0.859649
22 SIA NAG 0.479592 0.910714
23 18D 0.458824 0.796296
24 42D 0.458824 0.8
25 SIA GAL SIA BGC NGA CEQ 0.455882 0.8
26 CNP 0.454545 0.767857
27 BGC GAL CEQ SLB NGA GAL SIA SIA 0.452555 0.866667
28 MUS 0.451923 0.79661
29 SIA GAL NGA 0.445455 0.962264
30 SIA GAL A2G 0.440367 0.962264
31 NGA GAL SIA 0.440367 0.962264
32 SIA BGC GAL 0.436364 0.924528
33 BGC GAL SIA 0.436364 0.924528
34 NAG SIA GAL 0.436364 0.962264
35 SIA GAL NAG 0.436364 0.962264
36 SIA GAL BGC 0.436364 0.924528
37 SIA GAL GLC 0.436364 0.924528
38 GLA GLC SIA 0.436364 0.924528
39 BGC SIA GAL 0.436364 0.924528
40 GAL BGC SIA 0.436364 0.924528
41 NGC 0.435294 0.811321
42 MN0 0.431818 0.818182
43 NAG GAL SIA 0.428571 0.944444
44 SIA 2FG NAG 0.424779 0.894737
45 SIA NAG GAL 0.424779 0.910714
46 5N6 GAL 0.419048 0.925926
47 GAL TNR SIA 0.418803 0.927273
48 GAL SIA NGA GAL 0.418803 0.962264
49 GAL SIA NGA GAL SIA 0.418803 0.962264
50 SIA GLA NAG FUC 0.416667 0.962264
51 FUC NDG GAL SIA 0.416667 0.962264
52 NDG FUC SIA GAL 0.416667 0.962264
53 SIA GAL NAG FUC 0.416667 0.962264
54 SIA GAL NDG FUC 0.416667 0.962264
55 SIA GAL MAG FUC 0.416667 0.962264
56 NAG FUC SIA GAL 0.416667 0.962264
57 NGC MBG 0.413462 0.907407
58 SID 0.413043 0.785714
59 SIA WIA 0.407767 0.862069
60 SIA NAG GAL GAL 0.40678 0.944444
61 SIA GAL NGA GAL 0.40678 0.962264
62 GAL NGA GAL SIA 0.40678 0.962264
63 NXD 0.404255 0.793103
64 SIA GAL NDG SIA 0.403361 0.910714
65 SIA GAL NAG SIA 0.403361 0.944444
66 C5P SIA 0.403226 0.666667
67 425 0.401786 0.662338
68 SIA GAL NGS 0.4 0.784615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WBD; Ligand: SIA SIA SIA SIA SIA SIA SIA; Similar sites found: 9
This union binding pocket(no: 1) in the query (biounit: 3wbd.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5L3W GDP 0.003019 0.41335 2.43902
2 5IN3 G1P 0.01939 0.40279 2.74314
3 4XZ3 ACP 0.009959 0.41707 3.65854
4 2EUG URA 0.01861 0.40557 3.93013
5 2GK6 ADP 0.02376 0.40045 4.87805
6 1YRO UDP 0.006759 0.41878 6.50407
7 4AG5 ADP 0.02208 0.40121 6.50407
8 4LC1 GDP 0.01173 0.40463 7.12166
9 4TUO SIA GAL SIA GLC NGA 0.000295 0.42471 48.1818
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